De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions

Abstract

The gene numbers and evolutionary rates of birds were assumed to be much lower than those of mammals, which is in sharp contrast to the huge species number and morphological diversity of birds. It is therefore necessary to construct a complete avian genome and analyze its evolution. We constructed a chicken pan-genome from 20 de novo assembled genomes with high sequencing depth, and identified 1,335 protein-coding genes and 3,011 long noncoding RNAs not found in GRCg6a. The majority of these novel genes were detected across most individuals of the examined transcriptomes but were seldomly measured in each of the DNA sequencing data regardless of Illumina or PacBio technology. Furthermore, different from previous pan-genome models, most of these novel genes were overrepresented on chromosomal sub-telomeric regions and micro-chromosomes, surrounded by extremely high proportions of tandem repeats, which strongly blocks DNA sequencing. These hidden genes were proved to be shared by all chicken genomes, included many housekeeping genes, and enriched in immune pathways. Comparative genomics revealed the novel genes had three-fold elevated substitution rates than known ones, updating the knowledge about evolutionary rates in birds. Our study provides a framework for constructing a better chicken genome, which will contribute towards the understanding of avian evolution and improvement of poultry breeding.

A Gene Expression Atlas of Lohmann White Chickens

“…The publication of the chicken genome (Red junglefowl) in 2004 paved the way for understanding the genetic basis for distinguishing the different phenotypes of domesticated chickens from their wild relatives (K. 1, 2004). Recent studies using population resequencing data and de novo assembled-based chicken pan-genome have improved the sequencing quality for the assembly of complete avian genomes and revealed that the numbers of chicken genes are comparable to those of other tetrapod vertebrates and a new pan-genome pattern of birds (Li et al, 2022; Wang et al, 2021). In addition to pan-genome analyses, transcriptome annotation is crucial for a wide array of biological research areas (Cunningham et al, 2022).…”

Assembly of four indigenous chicken genomes reveal loss-of-function mutations as a critical driving force in chicken domestication and evolution

“…Moreover, we compared our 1,420 new genes with the 1,335 new genes recently found in 20 chicken genomes 11 . As shown in Figure 4f, our new genes with a mean length of 7,008 bp are much longer than the 1,335 new genes with a mean length of only 1,413 bp.…”

“…Moreover, hundreds of indigenous and commercial chicken breeds from all over the world have been resequenced using short-reads sequencing technologies 10 . Recently, Li, et al have assembled a pangenome for chicken using short reads, long reads and Hi-C data 11 . With a contig N50 of 5.89~16.72 Mb and a complete BUSCO 12 value of 92.4%~95.3% for a pan-genome, this assembly prevents the identi cation of the subtle differences in gene compositions of the chickens.…”

Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing

“…For instance, Warren et al (2017) added an additional 183 Mb sequences and assembled chromosomes 30-33 for the chicken reference genome. To fill the gaps of the chicken reference genome, recently two pangenomes were built that reported additional sequences absent from the GRCg6a reference genome (Wang K. et al, 2021;Li et al, 2022).…”